BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080907.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,657,881 number of mapped reads = 3,255,938 (89.01%) number of supplementary alignments = 34,309 (0.94%) number of secondary alignments = 0 number of mapped bases = 224,124,291 bp number of sequenced bases = 224,043,570 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,316 duplication rate = 3.56% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.0344 >>>>>>> ACTG content number of A's = 65,019,671 bp (29.02%) number of C's = 39,601,289 bp (17.68%) number of T's = 71,727,434 bp (32.01%) number of G's = 46,623,430 bp (20.81%) number of N's = 1,071,746 bp (0.48%) GC percentage = 38.49% >>>>>>> Mismatches and indels general error rate = 0.0113 number of mismatches = 2,510,824 number of insertions = 16,880 mapped reads with insertion percentage = 0.51% number of deletions = 49,348 mapped reads with deletion percentage = 1.5% homopolymer indels = 49.85% >>>>>>> Coverage mean coverageData = 0.0724X std coverageData = 0.4645X There is a 5.34% of reference with a coverageData >= 1X There is a 1.3% of reference with a coverageData >= 2X There is a 0.35% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 17233503 0.06914126404523582 0.680127703523598 chr2 243199373 19985168 0.08217606712333095 0.46382561871567696 chr3 198022430 16043926 0.08102075103310266 0.3661572985317955 chr4 191154276 15739884 0.0823412603126911 0.3753884100811583 chr5 180915260 14388095 0.07952947142214538 0.3642533203252476 chr6 171115067 13760218 0.08041499934076524 0.42816392512015317 chr7 159138663 12323793 0.0774405965695464 0.5507215879669238 chr8 146364022 11647191 0.07957687169870202 0.7623261516887242 chr9 141213431 9440310 0.06685136061880687 0.4795509404106155 chr10 135534747 10331768 0.07622966234629117 0.4299573995489402 chr11 135006516 10277567 0.07612645155586416 0.42321299149064856 chr12 133851895 10116866 0.0755825384466914 0.3598128121835428 chr13 115169878 7853761 0.06819283945060704 0.3360195607574026 chr14 107349540 6667830 0.06211326103493317 0.3482518208714308 chr15 102531392 6108836 0.05958015277896549 0.31334893630821836 chr16 90354753 5163784 0.0571501091923742 0.33544707822714215 chr17 81195210 4772787 0.058781632561822304 0.33964183760472577 chr18 78077248 5794936 0.0742205462979433 0.7460657029364159 chr19 59128983 3234803 0.05470757039741407 0.4870857503501562 chr20 63025520 4024858 0.06386076624199213 0.3293405612116058 chr21 48129895 2912728 0.06051806263030493 0.34823835621686 chr22 51304566 1884700 0.03673552174673888 0.2435268940546152 chrMT 16571 200749 12.114477098545652 6.206008840202574 chrX 155270560 13763303 0.08864077646142321 0.4066756784201614 chrY 59373566 452927 0.007628428449118249 0.13780854688741434